Contacts of the strand formed by residues 304 - 308 (chain A) in PDB entry 4N78
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A LEU* 3.7 12.1 - - - +
303A GLN* 1.3 88.2 - - + +
305A VAL* 1.3 71.3 + - - +
312A GLN* 3.8 4.5 - - + -
313A ILE 3.6 13.0 - - - +
314A GLU* 4.5 10.3 - - + +
315A LEU* 5.0 0.2 - - - -
410A GLU* 4.5 6.6 - - - +
413A SER* 3.2 35.8 + - - +
414A TRP* 4.0 26.3 - - + +
417A VAL* 3.5 38.4 - - + -
418A HIS* 4.3 4.7 - - + -
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A HIS* 3.7 35.4 - - + +
264A LEU* 4.3 7.6 - - + -
265A LYS* 3.8 21.8 - - + -
302A LEU* 3.8 20.0 - - + -
304A VAL* 1.3 79.5 - - - +
306A PRO* 1.3 72.3 - - + +
312A GLN* 3.8 0.9 - - - -
313A ILE* 2.9 47.4 + - + +
315A LEU* 4.0 13.2 - - + -
410A GLU* 5.1 0.4 - - + -
413A SER* 3.5 6.1 - - - -
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Residues in contact with PRO 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A HIS* 3.5 25.7 - - + +
265A LYS* 3.1 26.3 + - - +
305A VAL* 1.3 90.3 - - + +
307A LEU* 1.3 59.8 + - - +
308A PHE* 4.9 1.8 - - - +
309A GLY 4.8 9.6 - - - +
312A GLN* 3.2 22.0 - - - +
313A ILE* 4.2 0.2 - - - -
409A MET* 4.9 15.0 - - + +
410A GLU* 5.7 0.2 - - + -
412A TYR* 6.5 0.9 - - + -
413A SER* 4.0 9.9 - - - +
620A GLN* 6.5 1.6 - - + -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASN* 4.2 4.7 - - - +
169A ALA* 4.7 2.0 - - + +
170A VAL* 3.7 35.2 - - + +
173A GLU* 3.8 23.8 - - + -
265A LYS* 4.1 25.0 + - + +
305A VAL 3.5 1.4 + - - -
306A PRO* 1.3 73.8 - - - +
308A PHE* 1.3 68.6 + - - +
311A MET* 3.0 40.5 + - + +
312A GLN* 3.9 5.8 - - - +
313A ILE* 3.9 29.8 - - + -
317A ARG* 5.5 0.2 - - - +
318A TYR* 4.8 10.1 - - - +
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Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLN* 3.6 26.9 - - - -
80A ALA* 3.5 32.8 - - + -
81A VAL* 3.9 10.1 - - + -
84A TYR* 3.4 44.0 - + + -
170A VAL* 3.8 26.9 - - + -
174A LEU* 4.0 6.3 - - + -
306A PRO* 3.8 1.1 - - - -
307A LEU* 1.3 81.0 - - - +
309A GLY* 1.3 69.9 + - - +
310A ASP 3.4 0.2 + - - -
311A MET* 3.0 34.4 + - + +
682A PHE* 4.3 12.8 - + - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il